Burkholderia cepacia lipase (lipase PS-D) catalysed acylation with 3,3-difluoro-4-phenyl-, -thiophen-3-yl- and -4-pyridylazetidin-2-ones was examined for the formation of N-Boc-protected 6-O-acylated sugar–β-amino acid conjugates from methyl α-D-galacto-,-gluco- and mannopyranosides and Boc₂O. The 6-O-acylated glycopyranoside–β-amino acid conjugates were isolated and characterized. The low solubility of the gluco- and mannopyranosides and the high reactivity of the pyridylazetidinone restricted product formation. Activation of the β-lactam ring by the presence of fluorine substituents was shown to be necessary for the enzymatic acylation reaction. The (S)-enantiomers of the racemic β-lactam substrates reacted with the sugars.